wikipathways Schema Extraction¶

This notebook demonstrates RDF schema extraction from the wikipathways SPARQL endpoint by discovering or querying for VoID (Vocabulary of Interlinked Datasets) descriptions and some downstream uses.

Discover or get VoID Schema¶

No suitable existing VoID found, generating new VoID...
Starting query: class_partitions

Finished query: class_partitions (took 0.51s)
Starting query: property_partitions

Finished query: property_partitions (took 2.83s)
Starting query: datatype_partitions

Finished query: datatype_partitions (took 35.99s)
VoID description saved to /home/runner/work/rdfsolve/rdfsolve/notebooks/schema_extraction/../../docs/notebooks/wikipathways/wikipathways_generated_void.ttl

Class Partition Coverage Analysis¶

Query again to know how many times do we find instances of each "shape" in the dataset.

Counting instances per class...

Getting class mappings...

Calculating coverage statistics...

Coverage analysis exported to: /home/runner/work/rdfsolve/rdfsolve/notebooks/schema_extraction/../../docs/notebooks/wikipathways/wikipathways_coverage.csv
Saved to: /home/runner/work/rdfsolve/rdfsolve/notebooks/schema_extraction/../../docs/notebooks/wikipathways/wikipathways_coverage.csv

Schema Pattern Coverage Analysis¶

For each subject class type, calculate how many entities participate in each schema pattern divided by the total number of entities of that class type. This gives coverage ratios showing what percentage of entities actually use each relationship pattern.

Average pattern coverage: 25.2%
Patterns with >50% coverage: 177/833
Exported to: /home/runner/work/rdfsolve/rdfsolve/notebooks/schema_extraction/../../docs/notebooks/wikipathways/wikipathways_pattern_coverage.csv

LinkML¶

LinkML saved to /home/runner/work/rdfsolve/rdfsolve/notebooks/schema_extraction/../../docs/notebooks/wikipathways/wikipathways_linkml_schema.yaml

Mermaid diagram for LinkML Schema¶

Parsed LinkML schema: Classes = 39 Slots = 47

erDiagram
Anchor {

}
AnnotationProperty {

}
Axiom {

}
Binding {

}
Catalysis {

}
Class {

}
Collection {

}
Comment {

}
Complex {

}
ComplexBinding {

}
ConceptScheme {

}
Conversion {

}
DataNode {

}
DatatypeProperty {

}
DirectedInteraction {

}
GeneProduct {

}
GraphicalLine {

}
Group {

}
Image {

}
InfoBox {

}
Inhibition {

}
Interaction {

}
Label {

}
Metabolite {

}
ObjectProperty {

}
Ontology {

}
Pathway {

}
Person {

}
Point {

}
Protein {

}
PublicationReference {

}
PublicationXref {

}
Restriction {

}
Rna {

}
Shape {

}
State {

}
Stimulation {

}
TranscriptionTranslation {

}
Translocation {

}

Anchor ||--|o Class : "rdf_type"
Anchor ||--|o Pathway : "dcterms_isPartOf"
AnnotationProperty ||--|o AnnotationProperty : "rdfs_subPropertyOf"
Axiom ||--|o AnnotationProperty : "oboinowl_hasSynonymType"
Axiom ||--|o AnnotationProperty : "owl_annotatedProperty"
Axiom ||--|o ObjectProperty : "owl_annotatedSource"
Binding ||--|o Class : "rdf_type"
Binding ||--|o Complex : "participants"
Binding ||--|o DataNode : "source"
Binding ||--|o DataNode : "target"
Binding ||--|o Pathway : "dcterms_isPartOf"
Binding ||--|o PublicationReference : "dcterms_references"
Binding ||--|o PublicationXref : "dcterms_bibliographicCitation"
Catalysis ||--|o Class : "rdf_type"
Catalysis ||--|o Complex : "participants"
Catalysis ||--|o DataNode : "source"
Catalysis ||--|o DataNode : "target"
Catalysis ||--|o Pathway : "dcterms_isPartOf"
Catalysis ||--|o PublicationReference : "dcterms_references"
Class ||--|o AnnotationProperty : "oboinowl_inSubset"
Class ||--|o Class : "iao_0100001"
Class ||--|o Class : "owl_disjointWith"
Class ||--|o Class : "rdfs_subClassOf"
Class ||--|o ConceptScheme : "skos_inScheme"
Collection ||--|o Class : "diseaseOntologyTag"
Collection ||--|o Class : "ontologyTag"
Collection ||--|o Class : "pathwayOntologyTag"
Collection ||--|o Class : "rdf_type"
Collection ||--|o DataNode : "dc_identifier"
Collection ||--|o Image : "foaf_img"
Collection ||--|o PublicationReference : "cito_cites"
Collection ||--|o PublicationReference : "dcterms_references"
Comment ||--|o Class : "rdf_type"
Comment ||--|o Pathway : "dcterms_isPartOf"
Complex ||--|o Class : "rdf_type"
Complex ||--|o Complex : "bdbEntrezGene"
Complex ||--|o Complex : "bdbUniprot"
Complex ||--|o Complex : "participants"
Complex ||--|o DataNode : "bdbComplexPortal"
Complex ||--|o DataNode : "bdbHgncSymbol"
Complex ||--|o DataNode : "bdbReactome"
Complex ||--|o DataNode : "dc_identifier"
Complex ||--|o Pathway : "dcterms_isPartOf"
Complex ||--|o PublicationReference : "dcterms_references"
Complex ||--|o PublicationXref : "dcterms_bibliographicCitation"
Complex ||--|o Rna : "bdbEnsembl"
ComplexBinding ||--|o Class : "rdf_type"
ComplexBinding ||--|o Complex : "participants"
ComplexBinding ||--|o Pathway : "dcterms_isPartOf"
ComplexBinding ||--|o PublicationXref : "dcterms_bibliographicCitation"
Conversion ||--|o Class : "rdf_type"
Conversion ||--|o Complex : "participants"
Conversion ||--|o DataNode : "source"
Conversion ||--|o DataNode : "target"
Conversion ||--|o Pathway : "dcterms_isPartOf"
Conversion ||--|o PublicationReference : "dcterms_references"
DataNode ||--|o Class : "rdf_type"
DataNode ||--|o Comment : "hasComment"
DataNode ||--|o Complex : "bdbEntrezGene"
DataNode ||--|o Complex : "bdbUniprot"
DataNode ||--|o Complex : "participants"
DataNode ||--|o DataNode : "bdbComplexPortal"
DataNode ||--|o DataNode : "bdbHgncSymbol"
DataNode ||--|o DataNode : "bdbHmdb"
DataNode ||--|o DataNode : "bdbInChIKey"
DataNode ||--|o DataNode : "bdbKeggCompound"
DataNode ||--|o DataNode : "bdbLipidMaps"
DataNode ||--|o DataNode : "bdbReactome"
DataNode ||--|o DataNode : "dc_identifier"
DataNode ||--|o DataNode : "rdfs_seeAlso"
DataNode ||--|o Metabolite : "bdbChEBI"
DataNode ||--|o Metabolite : "bdbChemspider"
DataNode ||--|o Pathway : "dcterms_isPartOf"
DataNode ||--|o Pathway : "pav_hasVersion"
DataNode ||--|o Person : "dc_creator"
DataNode ||--|o PublicationReference : "dcterms_references"
DataNode ||--|o PublicationReference : "hasPublicationXref"
DataNode ||--|o PublicationXref : "dcterms_bibliographicCitation"
DataNode ||--|o Rna : "bdbEnsembl"
DatatypeProperty ||--|o Class : "rdfs_range"
DatatypeProperty ||--|o ConceptScheme : "skos_inScheme"
DirectedInteraction ||--|o Class : "rdf_type"
DirectedInteraction ||--|o Complex : "participants"
DirectedInteraction ||--|o DataNode : "bdbHmdb"
DirectedInteraction ||--|o DataNode : "bdbReactome"
DirectedInteraction ||--|o DataNode : "source"
DirectedInteraction ||--|o DataNode : "target"
DirectedInteraction ||--|o Metabolite : "bdbChEBI"
DirectedInteraction ||--|o Pathway : "dcterms_isPartOf"
DirectedInteraction ||--|o PublicationReference : "dcterms_references"
GeneProduct ||--|o Class : "rdf_type"
GeneProduct ||--|o Complex : "bdbEntrezGene"
GeneProduct ||--|o Complex : "bdbUniprot"
GeneProduct ||--|o DataNode : "bdbComplexPortal"
GeneProduct ||--|o DataNode : "bdbHgncSymbol"
GeneProduct ||--|o DataNode : "bdbKeggCompound"
GeneProduct ||--|o DataNode : "bdbReactome"
GeneProduct ||--|o DataNode : "dc_identifier"
GeneProduct ||--|o Metabolite : "bdbChEBI"
GeneProduct ||--|o Pathway : "dcterms_isPartOf"
GeneProduct ||--|o Pathway : "pav_hasVersion"
GeneProduct ||--|o Person : "dc_creator"
GeneProduct ||--|o PublicationReference : "dcterms_references"
GeneProduct ||--|o Rna : "bdbEnsembl"
GraphicalLine ||--|o Anchor : "hasAnchor"
GraphicalLine ||--|o Class : "rdf_type"
GraphicalLine ||--|o Comment : "hasComment"
GraphicalLine ||--|o Pathway : "dcterms_isPartOf"
GraphicalLine ||--|o Point : "hasPoint"
GraphicalLine ||--|o PublicationReference : "hasPublicationXref"
Group ||--|o Class : "rdf_type"
Group ||--|o Comment : "hasComment"
Group ||--|o PublicationReference : "hasPublicationXref"
InfoBox ||--|o Class : "rdf_type"
Inhibition ||--|o Class : "rdf_type"
Inhibition ||--|o Complex : "participants"
Inhibition ||--|o DataNode : "bdbHmdb"
Inhibition ||--|o DataNode : "source"
Inhibition ||--|o DataNode : "target"
Inhibition ||--|o Metabolite : "bdbChEBI"
Inhibition ||--|o Pathway : "dcterms_isPartOf"
Inhibition ||--|o PublicationReference : "dcterms_references"
Interaction ||--|o Anchor : "hasAnchor"
Interaction ||--|o Class : "rdf_type"
Interaction ||--|o Comment : "hasComment"
Interaction ||--|o Complex : "participants"
Interaction ||--|o DataNode : "bdbHmdb"
Interaction ||--|o DataNode : "bdbReactome"
Interaction ||--|o DataNode : "source"
Interaction ||--|o DataNode : "target"
Interaction ||--|o Metabolite : "bdbChEBI"
Interaction ||--|o Pathway : "dcterms_isPartOf"
Interaction ||--|o Point : "hasPoint"
Interaction ||--|o PublicationReference : "dcterms_references"
Interaction ||--|o PublicationReference : "hasPublicationXref"
Interaction ||--|o PublicationXref : "dcterms_bibliographicCitation"
Label ||--|o Class : "rdf_type"
Label ||--|o Comment : "hasComment"
Label ||--|o Pathway : "dcterms_isPartOf"
Label ||--|o PublicationReference : "hasPublicationXref"
Metabolite ||--|o Class : "rdf_type"
Metabolite ||--|o Complex : "bdbEntrezGene"
Metabolite ||--|o Complex : "bdbUniprot"
Metabolite ||--|o DataNode : "bdbHmdb"
Metabolite ||--|o DataNode : "bdbInChIKey"
Metabolite ||--|o DataNode : "bdbKeggCompound"
Metabolite ||--|o DataNode : "bdbLipidMaps"
Metabolite ||--|o DataNode : "bdbReactome"
Metabolite ||--|o DataNode : "dc_identifier"
Metabolite ||--|o DataNode : "rdfs_seeAlso"
Metabolite ||--|o Metabolite : "bdbChEBI"
Metabolite ||--|o Metabolite : "bdbChemspider"
Metabolite ||--|o Pathway : "dcterms_isPartOf"
Metabolite ||--|o PublicationReference : "dcterms_references"
ObjectProperty ||--|o Class : "rdfs_domain"
ObjectProperty ||--|o Class : "rdfs_range"
ObjectProperty ||--|o Class : "rdfs_subClassOf"
ObjectProperty ||--|o ConceptScheme : "skos_inScheme"
Pathway ||--|o Class : "diseaseOntologyTag"
Pathway ||--|o Class : "ontologyTag"
Pathway ||--|o Class : "pathwayOntologyTag"
Pathway ||--|o Class : "rdf_type"
Pathway ||--|o Complex : "bdbEntrezGene"
Pathway ||--|o Complex : "bdbUniprot"
Pathway ||--|o DataNode : "bdbHgncSymbol"
Pathway ||--|o DataNode : "dc_identifier"
Pathway ||--|o Image : "foaf_img"
Pathway ||--|o Pathway : "dcterms_isPartOf"
Pathway ||--|o Pathway : "pav_hasVersion"
Pathway ||--|o Person : "dc_creator"
Pathway ||--|o PublicationReference : "cito_cites"
Pathway ||--|o PublicationReference : "dcterms_references"
Pathway ||--|o Rna : "bdbEnsembl"
Point ||--|o Class : "rdf_type"
Point ||--|o Pathway : "dcterms_isPartOf"
Protein ||--|o Class : "rdf_type"
Protein ||--|o Complex : "bdbEntrezGene"
Protein ||--|o Complex : "bdbUniprot"
Protein ||--|o DataNode : "bdbHgncSymbol"
Protein ||--|o DataNode : "bdbReactome"
Protein ||--|o DataNode : "dc_identifier"
Protein ||--|o Metabolite : "bdbChEBI"
Protein ||--|o Pathway : "dcterms_isPartOf"
Protein ||--|o PublicationReference : "dcterms_references"
Protein ||--|o Rna : "bdbEnsembl"
PublicationReference ||--|o Class : "rdf_type"
PublicationReference ||--|o Pathway : "dcterms_isPartOf"
PublicationReference ||--|o PublicationReference : "cito_cites"
PublicationReference ||--|o PublicationReference : "foaf_page"
PublicationXref ||--|o Class : "rdf_type"
PublicationXref ||--|o Pathway : "dcterms_isPartOf"
Restriction ||--|o Class : "owl_someValuesFrom"
Restriction ||--|o ObjectProperty : "owl_onProperty"
Rna ||--|o Class : "rdf_type"
Rna ||--|o Complex : "bdbEntrezGene"
Rna ||--|o Complex : "bdbUniprot"
Rna ||--|o DataNode : "bdbHgncSymbol"
Rna ||--|o DataNode : "bdbKeggCompound"
Rna ||--|o DataNode : "dc_identifier"
Rna ||--|o Metabolite : "bdbChEBI"
Rna ||--|o Pathway : "dcterms_isPartOf"
Rna ||--|o PublicationReference : "dcterms_references"
Rna ||--|o Rna : "bdbEnsembl"
Shape ||--|o Class : "rdf_type"
Shape ||--|o Comment : "hasComment"
Shape ||--|o Pathway : "dcterms_isPartOf"
Shape ||--|o PublicationReference : "hasPublicationXref"
State ||--|o Class : "rdf_type"
State ||--|o Comment : "hasComment"
State ||--|o DataNode : "stateOf"
State ||--|o PublicationReference : "hasPublicationXref"
Stimulation ||--|o Class : "rdf_type"
Stimulation ||--|o Complex : "participants"
Stimulation ||--|o DataNode : "source"
Stimulation ||--|o DataNode : "target"
Stimulation ||--|o Pathway : "dcterms_isPartOf"
Stimulation ||--|o PublicationReference : "dcterms_references"
TranscriptionTranslation ||--|o Class : "rdf_type"
TranscriptionTranslation ||--|o Complex : "participants"
TranscriptionTranslation ||--|o DataNode : "source"
TranscriptionTranslation ||--|o DataNode : "target"
TranscriptionTranslation ||--|o Pathway : "dcterms_isPartOf"
TranscriptionTranslation ||--|o PublicationReference : "dcterms_references"
Translocation ||--|o Class : "rdf_type"
Translocation ||--|o Complex : "participants"
Translocation ||--|o DataNode : "source"
Translocation ||--|o DataNode : "target"
Translocation ||--|o Pathway : "dcterms_isPartOf"

LinkML pyDantic Model Generation¶

Found 37 Pydantic model classes for schema.

All 37 generated Pydantic classes:

=== Anchor ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]

=== AnnotationProperty ===
  rdfs_subPropertyOf: typing.Optional[AnnotationProperty]

=== Axiom ===
  owl_annotatedSource: typing.Optional[ObjectProperty]
  owl_annotatedProperty: typing.Optional[AnnotationProperty]
  oboinowl_hasSynonymType: typing.Optional[AnnotationProperty]

=== Binding ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  source: typing.Optional[DataNode]
  target: typing.Optional[DataNode]
  dcterms_bibliographicCitation: typing.Optional[PublicationXref]

=== Catalysis ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  source: typing.Optional[DataNode]
  target: typing.Optional[DataNode]

=== Class ===
  rdfs_subClassOf: typing.Optional[Class]
  skos_inScheme: typing.Optional[ConceptScheme]
  oboinowl_inSubset: typing.Optional[AnnotationProperty]
  iao_0100001: typing.Optional[Class]
  owl_disjointWith: typing.Optional[Class]

=== Collection ===
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  cito_cites: typing.Optional[PublicationReference]
  dc_identifier: typing.Optional[DataNode]
  diseaseOntologyTag: typing.Optional[Class]
  foaf_img: typing.Optional[Image]
  ontologyTag: typing.Optional[Class]
  pathwayOntologyTag: typing.Optional[Class]

=== Comment ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]

=== Complex ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  bdbReactome: typing.Optional[DataNode]
  dc_identifier: typing.Optional[DataNode]
  dcterms_bibliographicCitation: typing.Optional[PublicationXref]
  bdbComplexPortal: typing.Optional[DataNode]
  bdbEntrezGene: typing.Optional[Complex]
  bdbEnsembl: typing.Optional[Rna]
  bdbHgncSymbol: typing.Optional[DataNode]
  bdbUniprot: typing.Optional[Complex]

=== ComplexBinding ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_bibliographicCitation: typing.Optional[PublicationXref]

=== Conversion ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  source: typing.Optional[DataNode]
  target: typing.Optional[DataNode]

=== DataNode ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  bdbChEBI: typing.Optional[Metabolite]
  bdbHmdb: typing.Optional[DataNode]
  bdbReactome: typing.Optional[DataNode]
  dc_identifier: typing.Optional[DataNode]
  hasPublicationXref: typing.Optional[PublicationReference]
  hasComment: typing.Optional[Comment]
  dcterms_bibliographicCitation: typing.Optional[PublicationXref]
  bdbComplexPortal: typing.Optional[DataNode]
  bdbEntrezGene: typing.Optional[Complex]
  bdbEnsembl: typing.Optional[Rna]
  bdbHgncSymbol: typing.Optional[DataNode]
  bdbUniprot: typing.Optional[Complex]
  pav_hasVersion: typing.Optional[Pathway]
  bdbLipidMaps: typing.Optional[DataNode]
  dc_creator: typing.Optional[Person]
  bdbKeggCompound: typing.Optional[DataNode]
  bdbChemspider: typing.Optional[Metabolite]
  rdfs_seeAlso: typing.Optional[DataNode]
  bdbInChIKey: typing.Optional[DataNode]

=== DatatypeProperty ===
  skos_inScheme: typing.Optional[ConceptScheme]
  rdfs_range: typing.Optional[Class]

=== DirectedInteraction ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  source: typing.Optional[DataNode]
  target: typing.Optional[DataNode]
  bdbChEBI: typing.Optional[Metabolite]
  bdbHmdb: typing.Optional[DataNode]
  bdbReactome: typing.Optional[DataNode]

=== GeneProduct ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  bdbChEBI: typing.Optional[Metabolite]
  bdbReactome: typing.Optional[DataNode]
  dc_identifier: typing.Optional[DataNode]
  bdbComplexPortal: typing.Optional[DataNode]
  bdbEntrezGene: typing.Optional[Complex]
  bdbEnsembl: typing.Optional[Rna]
  bdbHgncSymbol: typing.Optional[DataNode]
  bdbUniprot: typing.Optional[Complex]
  pav_hasVersion: typing.Optional[Pathway]
  dc_creator: typing.Optional[Person]
  bdbKeggCompound: typing.Optional[DataNode]

=== GraphicalLine ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]
  hasPublicationXref: typing.Optional[PublicationReference]
  hasComment: typing.Optional[Comment]
  hasPoint: typing.Optional[Point]
  hasAnchor: typing.Optional[Anchor]

=== Group ===
  rdf_type: typing.Optional[Class]
  hasPublicationXref: typing.Optional[PublicationReference]
  hasComment: typing.Optional[Comment]

=== InfoBox ===
  rdf_type: typing.Optional[Class]

=== Inhibition ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  source: typing.Optional[DataNode]
  target: typing.Optional[DataNode]
  bdbChEBI: typing.Optional[Metabolite]
  bdbHmdb: typing.Optional[DataNode]

=== Interaction ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  source: typing.Optional[DataNode]
  target: typing.Optional[DataNode]
  bdbChEBI: typing.Optional[Metabolite]
  bdbHmdb: typing.Optional[DataNode]
  bdbReactome: typing.Optional[DataNode]
  hasPublicationXref: typing.Optional[PublicationReference]
  hasComment: typing.Optional[Comment]
  hasPoint: typing.Optional[Point]
  hasAnchor: typing.Optional[Anchor]
  dcterms_bibliographicCitation: typing.Optional[PublicationXref]

=== Label ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]
  hasPublicationXref: typing.Optional[PublicationReference]
  hasComment: typing.Optional[Comment]

=== LinkMLMeta ===
  root: dict[str, typing.Any]

=== Metabolite ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  bdbChEBI: typing.Optional[Metabolite]
  bdbHmdb: typing.Optional[DataNode]
  bdbReactome: typing.Optional[DataNode]
  dc_identifier: typing.Optional[DataNode]
  bdbEntrezGene: typing.Optional[Complex]
  bdbUniprot: typing.Optional[Complex]
  bdbLipidMaps: typing.Optional[DataNode]
  bdbKeggCompound: typing.Optional[DataNode]
  bdbChemspider: typing.Optional[Metabolite]
  rdfs_seeAlso: typing.Optional[DataNode]
  bdbInChIKey: typing.Optional[DataNode]

=== ObjectProperty ===
  rdfs_subClassOf: typing.Optional[Class]
  skos_inScheme: typing.Optional[ConceptScheme]
  rdfs_range: typing.Optional[Class]
  rdfs_domain: typing.Optional[Class]

=== Pathway ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  cito_cites: typing.Optional[PublicationReference]
  dc_identifier: typing.Optional[DataNode]
  diseaseOntologyTag: typing.Optional[Class]
  foaf_img: typing.Optional[Image]
  ontologyTag: typing.Optional[Class]
  pathwayOntologyTag: typing.Optional[Class]
  bdbEntrezGene: typing.Optional[Complex]
  bdbEnsembl: typing.Optional[Rna]
  bdbHgncSymbol: typing.Optional[DataNode]
  bdbUniprot: typing.Optional[Complex]
  pav_hasVersion: typing.Optional[Pathway]
  dc_creator: typing.Optional[Person]

=== Point ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]

=== Protein ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  bdbChEBI: typing.Optional[Metabolite]
  bdbReactome: typing.Optional[DataNode]
  dc_identifier: typing.Optional[DataNode]
  bdbEntrezGene: typing.Optional[Complex]
  bdbEnsembl: typing.Optional[Rna]
  bdbHgncSymbol: typing.Optional[DataNode]
  bdbUniprot: typing.Optional[Complex]

=== PublicationReference ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]
  cito_cites: typing.Optional[PublicationReference]
  foaf_page: typing.Optional[PublicationReference]

=== PublicationXref ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]

=== Restriction ===
  owl_someValuesFrom: typing.Optional[Class]
  owl_onProperty: typing.Optional[ObjectProperty]

=== Rna ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  bdbChEBI: typing.Optional[Metabolite]
  dc_identifier: typing.Optional[DataNode]
  bdbEntrezGene: typing.Optional[Complex]
  bdbEnsembl: typing.Optional[Rna]
  bdbHgncSymbol: typing.Optional[DataNode]
  bdbUniprot: typing.Optional[Complex]
  bdbKeggCompound: typing.Optional[DataNode]

=== RootModel ===
  root: ~RootModelRootType

=== Shape ===
  dcterms_isPartOf: typing.Optional[Pathway]
  rdf_type: typing.Optional[Class]
  hasPublicationXref: typing.Optional[PublicationReference]
  hasComment: typing.Optional[Comment]

=== State ===
  rdf_type: typing.Optional[Class]
  hasPublicationXref: typing.Optional[PublicationReference]
  hasComment: typing.Optional[Comment]
  stateOf: typing.Optional[DataNode]

=== Stimulation ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  source: typing.Optional[DataNode]
  target: typing.Optional[DataNode]

=== TranscriptionTranslation ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  dcterms_references: typing.Optional[PublicationReference]
  source: typing.Optional[DataNode]
  target: typing.Optional[DataNode]

=== Translocation ===
  dcterms_isPartOf: typing.Optional[Pathway]
  participants: typing.Optional[Complex]
  rdf_type: typing.Optional[Class]
  source: typing.Optional[DataNode]
  target: typing.Optional[DataNode]

	subject_class	subject_uri	property	property_uri	object_class	object_uri
22	owl:Class	http://www.w3.org/2002/07/owl#Class	rdfs:subClassOf	http://www.w3.org/2000/01/rdf-schema#subClassOf	owl:Class	http://www.w3.org/2002/07/owl#Class
23	owl:ObjectProperty	http://www.w3.org/2002/07/owl#ObjectProperty	rdfs:subClassOf	http://www.w3.org/2000/01/rdf-schema#subClassOf	owl:ObjectProperty	http://www.w3.org/2002/07/owl#ObjectProperty
24	owl:Class	http://www.w3.org/2002/07/owl#Class	skos:inScheme	http://www.w3.org/2004/02/skos/core#inScheme	skos:ConceptScheme	http://www.w3.org/2004/02/skos/core#ConceptScheme
25	owl:Class	http://www.w3.org/2002/07/owl#Class	skos:inScheme	http://www.w3.org/2004/02/skos/core#inScheme	owl:Ontology	http://www.w3.org/2002/07/owl#Ontology
26	owl:DatatypeProperty	http://www.w3.org/2002/07/owl#DatatypeProperty	skos:inScheme	http://www.w3.org/2004/02/skos/core#inScheme	skos:ConceptScheme	http://www.w3.org/2004/02/skos/core#ConceptScheme
...	...	...	...	...	...	...
850	PublicationReference	http://vocabularies.wikipathways.org/wp#Public...	foaf:page	http://xmlns.com/foaf/0.1/page	PublicationReference	http://vocabularies.wikipathways.org/wp#Public...
856	owl:Axiom	http://www.w3.org/2002/07/owl#Axiom	owl:annotatedSource	http://www.w3.org/2002/07/owl#annotatedSource	owl:ObjectProperty	http://www.w3.org/2002/07/owl#ObjectProperty
857	owl:Axiom	http://www.w3.org/2002/07/owl#Axiom	owl:annotatedSource	http://www.w3.org/2002/07/owl#annotatedSource	owl:Class	http://www.w3.org/2002/07/owl#Class
866	owl:Axiom	http://www.w3.org/2002/07/owl#Axiom	owl:annotatedProperty	http://www.w3.org/2002/07/owl#annotatedProperty	owl:AnnotationProperty	http://www.w3.org/2002/07/owl#AnnotationProperty
868	owl:Axiom	http://www.w3.org/2002/07/owl#Axiom	oboinowl:hasSynonymType	http://www.geneontology.org/formats/oboInOwl#h...	owl:AnnotationProperty	http://www.w3.org/2002/07/owl#AnnotationProperty

	subject_class	subject_uri	property	property_uri	object_class	object_uri
count	833	833	833	833	833	833
unique	35	37	47	47	35	37
top	DataNode	http://vocabularies.wikipathways.org/wp#DataNode	dcterms:isPartOf	http://purl.org/dc/terms/isPartOf	DataNode	http://vocabularies.wikipathways.org/wp#DataNode
freq	84	79	167	167	113	109

	subject_class	property	object_class	coverage_percent
4	owl:DatatypeProperty	skos:inScheme	skos:ConceptScheme	100.0
371	DirectedInteraction	source	DataNode	100.0
337	TranscriptionTranslation	rdf:type	owl:Class	100.0
336	Stimulation	rdf:type	owl:Class	100.0
338	Translocation	rdf:type	owl:Class	100.0
67	ComplexBinding	dcterms:isPartOf	Pathway	100.0
65	Complex	dcterms:isPartOf	skos:Collection	100.0
335	Rna	rdf:type	owl:Class	100.0
327	DataNode	rdf:type	owl:Class	100.0
328	GeneProduct	rdf:type	owl:Class	100.0